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gnu: checkm: Rename and update to 1.1.3. 

Renamed from python2-checkm-genome to checkm to better reflect its
status as standalone-application and support for Python 3.

* gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to…
(checkm): …here and update to 1.1.3.
[propagated-inputs]: Move to inputs.
[inputs]: Use Python 3 dependencies.
[home-page]: Point to real home-page.
master
Lars-Dominik Braun 2021-07-20 11:50:31 +02:00
parent 18a02fe7ca
commit 086c6800cf
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1 changed files with 20 additions and 13 deletions
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@ -13061,28 +13061,32 @@ downstream analysis.")
("taxtastic" ,taxtastic))) ("taxtastic" ,taxtastic)))
(synopsis "Pplacer Python scripts"))) (synopsis "Pplacer Python scripts")))
(define-public python2-checkm-genome (define-public checkm
(package (package
(name "python2-checkm-genome") (name "checkm")
(version "1.0.13") (version "1.1.3")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (pypi-uri "checkm-genome" version)) (uri (pypi-uri "checkm-genome" version))
(sha256 (sha256
(base32 (base32
"0bm8gpxjmzxsxxl8lzwqhgx8g1dlnmp6znz7wv3hgb0gdjbf9dzz")))) "0i2nnki639hgjag17wlva2x0ymn37b4krqsf6akxddykhfbkdnkz"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:python ,python-2 `(#:tests? #f ; Some tests fail for unknown reasons.
#:tests? #f)) ; some tests are interactive #:phases
(propagated-inputs (modify-phases %standard-phases
`(("python-dendropy" ,python2-dendropy) (add-before 'check 'set-HOME
("python-matplotlib" ,python2-matplotlib) (lambda _
("python-numpy" ,python2-numpy) (setenv "HOME" "/tmp"))))))
("python-pysam" ,python2-pysam) (inputs
("python-scipy" ,python2-scipy))) `(("python-dendropy" ,python-dendropy)
(home-page "https://pypi.org/project/Checkm/") ("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
("python-pysam" ,python-pysam)
("python-scipy" ,python-scipy)))
(home-page "https://ecogenomics.github.io/CheckM/")
(synopsis "Assess the quality of putative genome bins") (synopsis "Assess the quality of putative genome bins")
(description (description
"CheckM provides a set of tools for assessing the quality of genomes "CheckM provides a set of tools for assessing the quality of genomes
@ -13097,6 +13101,9 @@ on marker set compatibility, similarity in genomic characteristics, and
proximity within a reference genome.") proximity within a reference genome.")
(license license:gpl3+))) (license license:gpl3+)))
(define-public python2-checkm-genome
(deprecated-package "python2-checkm-genome" checkm))
(define-public umi-tools (define-public umi-tools
(package (package
(name "umi-tools") (name "umi-tools")